Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues
Aptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current syste...
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| Format: | Article |
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MDPI AG
2020-02-01
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| Series: | Sensors |
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| Online Access: | https://www.mdpi.com/1424-8220/20/3/915 |
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| author | Snizhana O. Zaitseva Nadezhda S. Baleeva Timofei S. Zatsepin Ivan N. Myasnyanko Anton V. Turaev Galina E. Pozmogova Alexei A. Khrulev Anna M. Varizhuk Mikhail S. Baranov Andrey V. Aralov |
| author_facet | Snizhana O. Zaitseva Nadezhda S. Baleeva Timofei S. Zatsepin Ivan N. Myasnyanko Anton V. Turaev Galina E. Pozmogova Alexei A. Khrulev Anna M. Varizhuk Mikhail S. Baranov Andrey V. Aralov |
| author_sort | Snizhana O. Zaitseva |
| collection | DOAJ |
| description | Aptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current systems are limited by relatively low enhancement of fluorescence upon dye binding. Here, we added duplex modules to G4 structures, which supposedly cause the formation of a dye-binding cavity between two modules. Screening of multiple synthetic GFP chromophore analogues and variation of the duplex module resulted in the selection of dyes that light up after complex formation with two-module structures and their RNA analogues by up to 20 times compared to parent G4s. We demonstrated that the short duplex part in TBA25 is preferable for fluorescence light up in comparison to parent TBA15 molecule as well as TBA31 and TBA63 stabilized by longer duplexes. Duplex part of TBA25 may be partially unfolded and has reduced rigidity, which might facilitate optimal dye positioning in the joint between G4 and the duplex. We demonstrated dye enhancement after binding to modified TBA, LTR-III, and Tel23a G4 structures and propose that such architecture of short duplex-G4 signaling elements will enforce the development of improved aptasensors. |
| first_indexed | 2024-04-14T01:39:50Z |
| format | Article |
| id | doaj.art-dfb1e190431146f39e01d3107c3085c3 |
| institution | Directory Open Access Journal |
| issn | 1424-8220 |
| language | English |
| last_indexed | 2024-04-14T01:39:50Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Sensors |
| spelling | doaj.art-dfb1e190431146f39e01d3107c3085c32022-12-22T02:19:48ZengMDPI AGSensors1424-82202020-02-0120391510.3390/s20030915s20030915Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore AnaloguesSnizhana O. Zaitseva0Nadezhda S. Baleeva1Timofei S. Zatsepin2Ivan N. Myasnyanko3Anton V. Turaev4Galina E. Pozmogova5Alexei A. Khrulev6Anna M. Varizhuk7Mikhail S. Baranov8Andrey V. Aralov9Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaSkolkovo Institute of Science and Technology, Moscow 121205, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaFederal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, RussiaFederal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaFederal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, RussiaAptasensors became popular instruments in bioanalytical chemistry and molecular biology. To increase specificity, perspective signaling elements in aptasensors can be separated into a G-quadruplex (G4) part and a free fluorescent dye that lights up upon binding to the G4 part. However, current systems are limited by relatively low enhancement of fluorescence upon dye binding. Here, we added duplex modules to G4 structures, which supposedly cause the formation of a dye-binding cavity between two modules. Screening of multiple synthetic GFP chromophore analogues and variation of the duplex module resulted in the selection of dyes that light up after complex formation with two-module structures and their RNA analogues by up to 20 times compared to parent G4s. We demonstrated that the short duplex part in TBA25 is preferable for fluorescence light up in comparison to parent TBA15 molecule as well as TBA31 and TBA63 stabilized by longer duplexes. Duplex part of TBA25 may be partially unfolded and has reduced rigidity, which might facilitate optimal dye positioning in the joint between G4 and the duplex. We demonstrated dye enhancement after binding to modified TBA, LTR-III, and Tel23a G4 structures and propose that such architecture of short duplex-G4 signaling elements will enforce the development of improved aptasensors.https://www.mdpi.com/1424-8220/20/3/915green fluorescent protein (gfp) chromophorefluorogenic dyeg-quadruplexquadruplex-duplex junctionaptamerbiosensors |
| spellingShingle | Snizhana O. Zaitseva Nadezhda S. Baleeva Timofei S. Zatsepin Ivan N. Myasnyanko Anton V. Turaev Galina E. Pozmogova Alexei A. Khrulev Anna M. Varizhuk Mikhail S. Baranov Andrey V. Aralov Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues Sensors green fluorescent protein (gfp) chromophore fluorogenic dye g-quadruplex quadruplex-duplex junction aptamer biosensors |
| title | Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues |
| title_full | Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues |
| title_fullStr | Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues |
| title_full_unstemmed | Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues |
| title_short | Short Duplex Module Coupled to G-Quadruplexes Increases Fluorescence of Synthetic GFP Chromophore Analogues |
| title_sort | short duplex module coupled to g quadruplexes increases fluorescence of synthetic gfp chromophore analogues |
| topic | green fluorescent protein (gfp) chromophore fluorogenic dye g-quadruplex quadruplex-duplex junction aptamer biosensors |
| url | https://www.mdpi.com/1424-8220/20/3/915 |
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